Upgrade Suite

The goal of this repository is to provide a streamlined custom migration path for the i5k website from Tripal 2 to Tripal 3. It may serve as a good starting point for other sites, but you will likely have to customize it for your own needs. Please don't follow this guide blindly!

Upgrade Process

Below is a detailed explanation of the full migration process. I've written shell scripts to automate the process as best I can. Some manual steps, however, are still unavoidable. I've flagged those steps with "manual step".

So to summarize:

• Clone this repository somewhere inside your drupal site structure so drush commands will work.
• sh pre_migration.sh
• follow manual pre migration steps
• run tripal 2 -> 3 migration via GUI
• sh post_migration.sh
• follow manual post migration steps

Prior to migrating

• Upgrading Chado
  • The pre-migration script will run delete the extra views and tables.
  • Manual step: You will still need to run the actual migration at /admin/tripal/storage/chado/install.
• disable ckeditor and wysiwyg_filter
• Manual step: create new full and filtered html filters (read more here).

The migration itself

Follow the Tripal 2 to 3 Migration guide.

After migrating

• Install and enable Tripal Manage Analyses.
  • This module will provide new chado tables for you, namely an organism_analsyis linker table.
  • This module also includes gene fields, and fields to link organisms to analyses and vice versa.
• Install and enable Tripal HQ
  • This module Lets users submit Chado content in your site in a safe way.
• Install and enable field permissions
  • Use in combination with Tripal HQ to hide confusing fields (dbxref for example) from users.
  • See this guide on how to use and configure.
• Convert Drupal fields not handled by the Tripal migration to chado properties.
  • Done in migrate_node_fields.php.
• Convert node-based internal-links to "future proof" Chado-based links.
  • Done in convert_node_links_to_chado.php.
  • Messages printed are to provide an inventory of non-analysis links. You'll have the link and the Chado organism_id to add the link via Chado later if you desire.
• Convert Node links in analysis sourceuris to entities, and add the relationship to analysis_relationship
  • Done in convert_sourceuris_from_nodes.php;

Configuring fields

The Tripal user's guide has detailed instructions on how to configure fields.

Originally, I had exported my field configurations into deployable modules using the Drupal features module. However, when Tripal creates field groupings, it gives it a name with random numbers in the string. This means that after you upgrade from Tripal 2 to Tripal 3 on your site, your field group names will be incompatible with mine. You can still use Drupal features, but the starting feature must be exported from a copy of your database, or, you must delete your feature groups prior to enabling the feature module.

Field configuration modules (DONT USE without first deleting your field groupings or renaming the field group names in the modules)

• Organism
• Analysis